用翻译软件给大家翻译了一下：简单总结，病毒有ABC三个型，A在美国澳大利亚，B由A变异，武汉的主要是B，C主要在欧洲，也是变异来的。

附译文：研究绘制了COVID-19从中国和亚洲传播到澳大利亚、欧洲和北美的“早期超新星”的遗传突变图。研究人员说，他们的方法可以用来帮助识别无证件的感染源。

系统发育网络分析有助于识别未记录的COVID-19感染源

皮特-佛斯特来自英国剑桥和德国的研究人员利用基因网络技术重建了COVID-19在人类体内的早期“进化路径”——随着感染从武汉扩散到欧洲和北美。

通过分析首批160个完整的人类患者病毒基因组，科学家们绘制出了新冠状病毒通过变异传播的一些原始图谱，这些变异产生了不同的病毒谱系。

“有太多的快速突变，无法清晰地追踪COVID-19家族树。剑桥大学的遗传学家彼得·福斯特博士说：“我们使用了一种数学网络算法来同时可视化所有可能的树。”。

“这些技术主要是通过DNA绘制史前人类种群的活动图。我们认为这是第一次使用它们来追踪像COVID-19这样的冠状病毒的感染途径。”

研究小组使用了从2019年12月24日至2020年3月4日期间从世界各地取样的病毒基因组数据。这项研究揭示了COVID-19的三个不同的“变体”，由密切相关的谱系组成，他们将其标记为“A”、“B”和“C”。

福斯特和他的同事们发现，与蝙蝠中发现的COVID-19最接近的一种类型——“A”型，即“原始人类病毒基因组”存在于武汉，但令人惊讶的是，它并不是武汉市的主要病毒类型。

据报道，在居住在武汉的美国人中发现了“A”的变异版本，在美国和澳大利亚的患者中发现了大量的A型病毒。

武汉的主要病毒类型“B”在东亚各地的患者中普遍存在。然而，研究人员说，这种变异在没有进一步突变的情况下并没有在该地区传播太多，这意味着武汉发生了“创始事件”，或者东亚以外地区对这种COVID-19的“抵抗”。

“C”变异是主要的欧洲类型，在法国、意大利、瑞典和英国的早期患者中发现。该研究在中国大陆的样本中不存在，但在新加坡、香港和韩国都有。

新的分析还表明，最早将该病毒引入意大利的病毒之一是在1月27日通过第一次有记录的德国感染，而意大利早期的另一种感染途径与“新加坡群”有关。

重要的是，研究人员说，他们的基因网络技术准确地追踪了既定的感染途径：突变和病毒谱系在已知病例之间连接在一起。因此，科学家们认为，这些“系统发育”方法可以应用于最新的冠状病毒基因组测序，以帮助预测未来全球疾病传播和激增的热点。

剑桥大学麦克唐纳考古研究所（McDonald Institute of Archemical Research）以及该大学继续教育研究所（University of Continuous Education）的研究员福斯特说：“系统发育网络分析有可能有助于识别未登记的COVID-19感染源，然后将其隔离，以遏制该疾病在全球的进一步传播。”。

研究结果发表在今天的《美国国家科学院院刊》（PNAS）上。研究中使用的软件，以及超过1000个冠状病毒基因组和计数的分类，可在www.fluxus-technology.com上免费获得。

变异体“A”，与蝙蝠和穿山甲中发现的病毒最为密切相关，被研究人员称为“爆发的根源”。类型“B”是从“A”派生的，由两个突变分开，然后“C”又是“B”的“女儿”。

研究人员说，B变种在东亚的定位可能是“奠基人效应”的结果：在病毒的情况下，一种新型病毒是从一小部分孤立的感染群中产生的，这是一种遗传瓶颈。

福斯特认为还有另一个解释值得考虑。“武汉B型病毒可以在免疫或环境上适应东亚大部分人群。它可能需要变异以克服东亚以外的阻力。在这个初始阶段，我们似乎看到东亚地区的突变率比其他地区要慢。”他补充道：“我们详细描述的病毒网络是一种流行病早期阶段的快照，在COVID-19的进化路径被大量突变所掩盖之前。这就像是在行动中捕捉到一颗初生的超新星。”

自从今天的PNAS研究开始以来，研究小组已经将分析扩展到了1001个病毒基因组。福斯特说，虽然尚待同行评审，但最新的研究表明，COVID-19在人类中的首次感染和传播发生在9月中旬至12月初。

研究人员使用的系统发育网络方法（允许在一个简单的图表中同时可视化数百棵进化树）于1979年在新西兰率先提出，然后在1990年代由德国数学家发展起来。

这些技术引起了考古学家Colin Renfrew教授的注意，他是1998年新PNAS研究的合著者。伦弗鲁接着在剑桥大学建立了世界上最早的考古遗传学研究小组之一。

鏈接: https://www.cam.ac.uk/research/news/covid-19-genetic-network-analysis-provides-snapshot-of-pandemic-origins?from=timeline&isappinstalled=0

Study charts the “incipient supernova” of COVID-19 through genetic mutations as it spread from China and Asia to Australia, Europe and North America. Researchers say their methods could be used to help identify undocumented infection sources.

Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources

Peter Forster

Researchers from Cambridge, UK, and Germany have reconstructed the early “evolutionary paths” of COVID-19 in humans – as infection spread from Wuhan out to Europe and North America – using genetic network techniques.

By analysing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.

“There are too many rapid mutations to neatly trace a COVID-19 family tree. We used a mathematical network algorithm to visualise all the plausible trees simultaneously,” said geneticist Dr Peter Forster, lead author from the University of Cambridge.

“These techniques are mostly known for mapping the movements of prehistoric human populations through DNA. We think this is one of the first times they have been used to trace the infection routes of a coronavirus like COVID-19.”

The team used data from virus genomes sampled from across the world between 24 December 2019 and 4 March 2020. The research revealed three distinct “variants” of COVID-19, consisting of clusters of closely related lineages, which they label ‘A’, ‘B’ and ‘C’.

Forster and colleagues found that the closest type of COVID-19 to the one discovered in bats – type ‘A’, the “original human virus genome” – was present in Wuhan, but surprisingly was not the city’s predominant virus type.

Mutated versions of ‘A’ were seen in Americans reported to have lived in Wuhan, and a large number of A-type viruses were found in patients from the US and Australia.

Wuhan’s major virus type, ‘B’, was prevalent in patients from across East Asia. However, the variant didn’t travel much beyond the region without further mutations – implying a "founder event" in Wuhan, or “resistance” against this type of COVID-19 outside East Asia, say researchers.

The ‘C’ variant is the major European type, found in early patients from France, Italy, Sweden and England. It is absent from the study’s Chinese mainland sample, but seen in Singapore, Hong Kong and South Korea.

The new analysis also suggests that one of the earliest introductions of the virus into Italy came via the first documented German infection on January 27, and that another early Italian infection route was related to a “Singapore cluster”.

Importantly, the researchers say that their genetic networking techniques accurately traced established infection routes: the mutations and viral lineages joined the dots between known cases.

As such, the scientists argue that these “phylogenetic” methods could be applied to the very latest coronavirus genome sequencing to help predict future global hot spots of disease transmission and surge.

“Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources, which can then be quarantined to contain further spread of the disease worldwide,” said Forster, a fellow of the McDonald Institute of Archaeological Research at Cambridge, as well as the University’s Institute of Continuing Education.

The findings are published today in the journal Proceedings of the National Academy of Sciences (PNAS). The software used in the study, as well as classifications for over 1,000 coronavirus genomes and counting, is available free at www.fluxus-technology.com.

Variant ‘A’, most closely related to the virus found in both bats and pangolins, is described as “the root of the outbreak” by researchers. Type ‘B’ is derived from ‘A’, separated by two mutations, then ‘C’ is in turn a “daughter” of ‘B’.

Researchers say the localisation of the ‘B’ variant to East Asia could result from a “founder effect”: a genetic bottleneck that occurs when, in the case of a virus, a new type is established from a small, isolated group of infections.

Forster argues that there is another explanation worth considering. “The Wuhan B-type virus could be immunologically or environmentally adapted to a large section of the East Asian population. It may need to mutate to overcome resistance outside East Asia. We seem to see a slower mutation rate in East Asia than elsewhere, in this initial phase.”

He added: “The viral network we have detailed is a snapshot of the early stages of an epidemic, before the evolutionary paths of COVID-19 become obscured by vast numbers of mutations. It’s like catching an incipient supernova in the act.”

Since today’s PNAS study was conducted, the research team has extended its analysis to 1,001 viral genomes. While yet to be peer-reviewed, Forster says the latest work suggests that the first infection and spread among humans of COVID-19 occurred between mid-September and early December.

The phylogenetic network methods used by researchers – allowing the visualisation of hundreds of evolutionary trees simultaneously in one simple graph – were pioneered in New Zealand in 1979, then developed by German mathematicians in the 1990s.

These techniques came to the attention of archaeologist Professor Colin Renfrew, a co-author of the new PNAS study, in 1998. Renfrew went on to establish one of the first archaeogenetics research groups in the world at the University of Cambridge.

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